Mass spectrometry has become a major analytical tool in proteomic and biological research in general. Most protein identification strategies involving MS analyze proteolytic peptides (e.g. tryptic digests for mass fingerprinting in combination with tandem MS to confirm amino acid sequence and the presence of various posttranslational modifications. In most proteome studies, proteins are separated on electrophoretic gels and in-gel digestion extracts are subjected to MS analysis. Although matrix assisted laser desorption/ionization (MALDI) is very effective for screening high abundance proteins in complex samples, lower abundance peptides often remain undetected. Suppression effects are a common problem arising from the presence of multiple analytes competing for protons during the ionization process. Various separation methods have been coupled to mass spectrometry to improve identification of macrolecules. However, efficient coupling to MALDI have been more difficult. High throughput MALDI requires deposition of multiple sample drops on a MALDI target plate. Chen et al. (analytical Chemistry vol 76, No 4, 2004) have proposed a method for separating molecules within samples and depositing drops of the eluent on a MALDI target surface by using negative pressure. However, their apparatus comprises a cumbersome vacuum chamber box in which the MALDI target and the separation device are inserted. Drop deposition is made difficult by the limited number of degrees of freedom for displacing the tip of the separation device relative to the target. A similar arrangement with a subatmospheric deposition chamber is described in Karger et al. (U.S. Pat. Nos. 6,674,070 and 6,825,463) Accordingly better coupling of separating/drop deposition device and targets are needed.